Variant report

Variant	rs7209129
Chromosome Location	chr17:20919504-20919505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20919466-20921064	GM12891	blood:	n/a	n/a
2	POLR2A	chr17:20919379-20921064	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:20919453-20919728	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:20919400-20923329	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:20919392-20921129	GM12892	blood:	n/a	n/a
6	POLR2A	chr17:20919318-20920199	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:20919500-20919695	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:20919364-20919510	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr17:20919418-20921060	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:20917991-20921614	A549	lung:	n/a	n/a
11	POLR2A	chr17:20917596-20921783	K562	blood:	n/a	n/a
12	POLR2A	chr17:20919461-20919846	K562	blood:	n/a	n/a
13	POLR2A	chr17:20918057-20921119	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:20918951-20919785	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:20918559..20920846-chr17:20922682..20924740,2	K562	blood:
2	chr17:20916181..20917774-chr17:20918332..20921119,2	MCF-7	breast:
3	chr17:20918559..20920531-chr17:20920767..20924740,3	K562	blood:
4	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-7	chr17:20919461-20919862	NONHSAT052155
2	lnc-DHRS7B-7	chr17:20919473-20919862	l_1417_chr17:20919472-20934581_brain

No data

Variant related genes	Relation type
USP22	TF binding region
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1045162	0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1127814	0.88[ASN][1000 genomes]
rs12600703	0.89[JPT][hapmap]
rs12602058	0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12943067	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12946114	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531566	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17770614	0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2054464	0.91[ASN][1000 genomes]
rs2127095	0.91[ASN][1000 genomes]
rs2291034	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2364326	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4445951	0.89[ASN][1000 genomes]
rs4985814	0.87[ASN][1000 genomes]
rs4985815	0.85[ASN][1000 genomes]
rs4985816	0.87[ASN][1000 genomes]
rs4985948	0.83[YRI][hapmap]
rs4985959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985966	0.82[ASN][1000 genomes]
rs4985967	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985968	0.87[ASN][1000 genomes]
rs4985969	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4985970	0.87[ASN][1000 genomes]
rs4985971	0.87[ASN][1000 genomes]
rs56323013	0.87[ASN][1000 genomes]
rs58235085	0.87[ASN][1000 genomes]
rs59543297	0.89[ASN][1000 genomes]
rs59713572	0.84[ASN][1000 genomes]
rs6587111	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587114	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719093	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7207753	0.83[AFR][1000 genomes]
rs7213684	0.83[AFR][1000 genomes]
rs7216921	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7226229	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs8064435	0.82[MKK][hapmap]
rs899340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899341	0.85[AFR][1000 genomes]
rs9895277	0.89[AFR][1000 genomes]
rs9911289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7209129	USP22	cis	brain	BrainEAC
rs7209129	USP22	cis	inferior olivary nucleus	BrainEAC
rs7209129	USP22	cis	Liver	GTEx
rs7209129	SMCR7	cis	cerebellum	SCAN
rs7209129	USP22	cis	temporal cortex	BrainEAC
rs7209129	USP22	cis	frontal cortex	BrainEAC
rs7209129	USP22	cis	cerebellar cortex	BrainEAC
rs7209129	USP22	cis	occipital cortex	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20900200-20924000	Strong transcription	Fetal Stomach	stomach
2	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
3	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
4	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
5	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
6	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
7	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
9	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:20902000-20935400	Strong transcription	Dnd41	blood
16	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
18	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:20902400-20931600	Strong transcription	HMEC	breast
21	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:20902600-20925400	Strong transcription	NHEK	skin
26	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
33	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:20903400-20932000	Strong transcription	Liver	Liver
36	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:20903800-20924000	Strong transcription	Lung	lung
39	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:20904000-20928200	Strong transcription	A549	lung
41	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
43	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:20904600-20925200	Strong transcription	NH-A	brain
45	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
46	chr17:20905000-20923800	Strong transcription	Pancreas	Pancrea
47	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
49	chr17:20905200-20923400	Strong transcription	Aorta	Aorta
50	chr17:20905200-20926600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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